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- PDB-3taz: Crystal structure of NurA bound to dAMP and manganese -

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Basic information

Entry
Database: PDB / ID: 3taz
TitleCrystal structure of NurA bound to dAMP and manganese
ComponentsDNA double-strand break repair protein nurA
KeywordsHYDROLASE / Recombination
Function / homology
Function and homology information


exonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / metal ion binding
Similarity search - Function
DNA double-strand break repair nuclease NurA-like / NurA domain / NurA domain / NurA
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / : / DNA double-strand break repair nuclease NurA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 3.2 Å
AuthorsChae, J. / Kim, Y.C. / Cho, Y.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of the NurA-dAMP-Mn2+ complex
Authors: Chae, J. / Kim, Y.C. / Cho, Y.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jun 5, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA double-strand break repair protein nurA
B: DNA double-strand break repair protein nurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2456
Polymers107,7122
Non-polymers5334
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-53 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.158, 114.847, 123.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA double-strand break repair protein nurA / Putative uncharacterized protein


Mass: 53856.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1168 / Plasmid: pET-28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1N8
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% PEG 400, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15913 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 98.57 Å2
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→28.712 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 0 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 784 5.05 %
Rwork0.1912 --
obs0.1957 15536 98.07 %
all-15828 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.787 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 260.04 Å2 / Biso mean: 109.6429 Å2 / Biso min: 22 Å2
Baniso -1Baniso -2Baniso -3
1--4.676 Å20 Å2-0 Å2
2--16.5621 Å2-0 Å2
3----11.8861 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6981 0 30 9 7020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017132
X-RAY DIFFRACTIONf_angle_d1.4569623
X-RAY DIFFRACTIONf_dihedral_angle_d19.8862749
X-RAY DIFFRACTIONf_chiral_restr0.0921109
X-RAY DIFFRACTIONf_plane_restr0.0061205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2003-3.40050.33381170.229232294
3.4005-3.66250.32921310.2012238197
3.6625-4.03020.26961330.2006243399
4.0302-4.61130.28811360.1725246699
4.6113-5.80190.28151300.18852531100
5.8019-28.71290.25511370.192619100
Refinement TLS params.Method: refined / Origin x: 56.7886 Å / Origin y: 65.3059 Å / Origin z: 92.6556 Å
111213212223313233
T0.2532 Å20.0418 Å2-0.0389 Å2-0.2191 Å2-0.0457 Å2--0.2846 Å2
L0.836 °20.3242 °2-0.0741 °2-0.3827 °20.1843 °2--2.0896 °2
S0.0147 Å °-0.0917 Å °0.1202 Å °0.0016 Å °-0.1022 Å °0.0223 Å °0.0006 Å °0.1384 Å °0.0416 Å °
Refinement TLS groupSelection details: all

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